Early Antibiotics Disrupt Gut Microbiome in Infants

Cambridge, MA—What effect do early antibiotics have on infants? Potentially extensive, according to some new studies.

Research involving 80 infants found that the development of the human gut microbiome can be disrupted by antibiotics—as well as birth mode and diet.

The reports in Science Translational Medicine note that children treated and retreated with antibiotics during early life had lower microbial diversity and also harbored antibiotic resistance genes, albeit temporarily, after treatment.

Antibiotic treatment among children is routine in most parts of the world, with the average American child receiving three courses of antibiotics by the second year, according to background information in the article. It notes that gut microbiome disturbances have been linked to higher risk of obesity, diabetes, asthma, and to allergies later in life.

Multiple studies led by researchers from Massachusetts Institute of Technology (MIT) and Harvard University and by researchers from Aalto University School of Science in Espoo and the University of Helsinki, both in Finland, sought to better determine how the infant microbiome responds to and recovers from environmental effects, including those from antibiotic treatment, cesarean section versus vaginal delivery, and formula feeding versus breast-feeding.

In one study, researchers tracked the microbial development of 43 U.S. infants. For 2 years after birth, their stool samples were collected, as well as additional samples from their mothers before and after birth. Results indicate that antibiotics, cesarean delivery, and formula feeding can delay infants’ microbiome development and reduce bacterial diversity. The study also suggests that the mother's own microbiota, which is known to populate the infant gut during passage through the birth canal, also influences the healthy development of the infant’s microbiota, as do breast-feeding and skin contact.

In a second study analyzing stool samples collected from 39 children over 3 years, investigators found that repeated antibiotic treatment reduced gut microbial diversity while spurring a transient rise in antibiotic resistance genes.

The research also determined that, in the first few months of life, all infants born by cesarean section—as well as about 20% of those born by vaginal delivery—lack bacteroides to help regulate intestinal immunity, suggesting that birth mode and other factors can strongly influence bacterial diversity. Children treated with antibiotics had less diverse and less stable microbiota at the level of both species and strain. They also were more likely to develop antibiotic resistance genes that increased following antibiotic treatment, before sharply declining, according to the results.

The research also uncovered the surprising information that some infants as young as two months old have antibiotic resistance genes, even if they never have been exposed to antibiotics.